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Niroomand MP, Morgan JWR, Cafolla CT, Wales DJ. On the capacity and superposition of minima in neural network loss function landscapes. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1088/2632-2153/ac64e6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Minima of the loss function landscape (LFL) of a neural network are locally optimal sets of weights that extract and process information from the input data to make outcome predictions. In underparameterised networks, the capacity of the weights may be insufficient to fit all the relevant information. We demonstrate that different local minima specialise in certain aspects of the learning problem, and process the input information differently. This effect can be exploited using a meta-network in which the predictive power from multiple minima of the LFL is combined to produce a better classifier. With this approach, we can increase the area under the receiver operating characteristic curve by around
20
%
for a complex learning problem. We propose a theoretical basis for combining minima and show how a meta-network can be trained to select the representative that is used for classification of a specific data item. Finally, we present an analysis of symmetry-equivalent solutions to machine learning problems, which provides a systematic means to improve the efficiency of this approach.
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Jiang H, Xie X, Ban X, Gu Z, Cheng L, Hong Y, Li C, Li Z. Flexible Loop in Carbohydrate-Binding Module 48 Allosterically Modulates Substrate Binding of the 1,4-α-Glucan Branching Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5755-5763. [PMID: 33988022 DOI: 10.1021/acs.jafc.1c00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The 1,4-α-glucan branching enzyme (GBE, EC 2.4.1.18) catalyzes the formation of α-1,6 branching points in starch and plays a key role in synthesis. To obtain mechanistic insights into the catalytic action of the enzyme, we first determined the crystal structure of GBE from Rhodothermus obamensis STB05 (RoGBE) to a resolution of 2.39 Å (PDB ID: 6JOY). The structure consists of three domains: domain A, domain C, and the carbohydrate-binding module 48 (CBM48). An engineered truncated mutant lacking the CBM48 domain (ΔCBM48) showed significantly reduced ligand binding affinity and enzyme activity. Comparison of the structures of RoGBE with other GBEs showed that CBM48 of RoGBE had a longer flexible loop. Truncation of the flexible loops resulted in reduced binding affinity and activity, thereby substantiating the importance of the optimum loop structure for catalysis. In essence, our study shows that CBM48, especially the flexible loop, plays an important role in substrate binding and enzymatic activity of RoGBE. Further, based on the structural analysis, kinetics, and activity assays on wild type and mutants, as well as homology modeling, we proposed a mechanistic model (called the "lid model") to illustrate how the flexible loop triggers substrate binding, ultimately leading to catalysis.
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Affiliation(s)
- Haimin Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
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Barthels F, Schirmeister T, Kersten C. BANΔIT: B'-Factor Analysis for Drug Design and Structural Biology. Mol Inform 2020; 40:e2000144. [PMID: 32830452 PMCID: PMC7461025 DOI: 10.1002/minf.202000144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 12/02/2022]
Abstract
The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐based drug design since protein mobility changes have been associated with the quality of protein‐ligand interactions. With the BANΔIT (B’‐factor analysis and ΔB’ interpretation toolkit), we have developed a JavaScript‐based browser application that provides a graphical user interface for the normalization and analysis of B’‐factor profiles. To emphasize the usability for rational drug design applications, we have analyzed a selection of crystallographic protein‐ligand complexes and have given exemplary conclusions for further drug optimization including the development of a B’‐factor‐supported pharmacophore model for SARS CoV‐2 main protease inhibitors. BANΔIT is available online at https://bandit.uni‐mainz.de. The source code can be downloaded from https://github.com/FBarthels/BANDIT.
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Affiliation(s)
- Fabian Barthels
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christian Kersten
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128, Mainz, Germany
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Barnes CA, Shen Y, Ying J, Takagi Y, Torchia DA, Sellers JR, Bax A. Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy. J Am Chem Soc 2019; 141:9004-9017. [PMID: 31117653 PMCID: PMC6556874 DOI: 10.1021/jacs.9b03116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Although the α-helix has long been recognized as an all-important element of secondary structure, it generally requires stabilization by tertiary interactions with other parts of a protein's structure. Highly charged single α-helical (SAH) domains, consisting of a high percentage (>75%) of Arg, Lys, and Glu residues, are exceptions to this rule but have been difficult to characterize structurally. Our study focuses on the 68-residue medial tail domain of myosin-VI, which is found to contain a highly ordered α-helical structure extending from Glu-6 to Lys-63. High hydrogen exchange protection factors (15-150), small (ca. 4 Hz) 3 JHNHα couplings, and a near-perfect fit to an ideal model α-helix for its residual dipolar couplings (RDCs), measured in a filamentous phage medium, support the high regularity of this helix. Remarkably, the hydrogen exchange rates are far more homogeneous than the protection factors derived from them, suggesting that for these transiently broken helices the intrinsic exchange rates derived from the amino acid sequence are not appropriate reference values. 15N relaxation data indicate a very high degree of rotational diffusion anisotropy ( D∥/ D⊥ ≈ 7.6), consistent with the hydrodynamic behavior predicted for such a long, nearly straight α-helix. Alignment of the helix by a paramagnetic lanthanide ion attached to its N-terminal region shows a decrease in alignment as the distance from the tagging site increases. This decrease yields a precise measure for the persistence length of 224 ± 10 Å at 20 °C, supporting the idea that the role of the SAH helix is to act as an extension of the myosin-VI lever arm.
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ElGamacy M, Riss M, Zhu H, Truffault V, Coles M. Mapping Local Conformational Landscapes of Proteins in Solution. Structure 2019; 27:853-865.e5. [PMID: 30930065 DOI: 10.1016/j.str.2019.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/05/2018] [Accepted: 03/07/2019] [Indexed: 01/19/2023]
Abstract
The ability of proteins to adopt multiple conformational states is essential to their function, and elucidating the details of such diversity under physiological conditions has been a major challenge. Here we present a generalized method for mapping protein population landscapes by NMR spectroscopy. Experimental NOESY spectra are directly compared with a set of expectation spectra back-calculated across an arbitrary conformational space. Signal decomposition of the experimental spectrum then directly yields the relative populations of local conformational microstates. In this way, averaged descriptions of conformation can be eliminated. As the method quantitatively compares experimental and expectation spectra, it inherently delivers an R factor expressing how well structural models explain the input data. We demonstrate that our method extracts sufficient information from a single 3D NOESY experiment to perform initial model building, refinement, and validation, thus offering a complete de novo structure determination protocol.
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Affiliation(s)
- Mohammad ElGamacy
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Michael Riss
- Department of Informatics, Technical University of Munich, Boltzmannstrasse 3, 85748 Garching, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vincent Truffault
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.
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7
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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Vögeli B, Vugmeyster L. Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies. Chemphyschem 2019; 20:178-196. [PMID: 30110510 PMCID: PMC9206835 DOI: 10.1002/cphc.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 01/09/2023]
Abstract
Cross-correlated relaxation (CCR) in multiple-quantum coherences differs from other relaxation phenomena in its theoretical ability to be mediated across an infinite distance. The two interfering relaxation mechanisms may be dipolar interactions, chemical shift anisotropies, chemical shift modulations or quadrupolar interactions. These properties make multiple-quantum CCR an attractive probe for structure and dynamics of biomacromolecules not accessible from other measurements. Here, we review the use of multiple-quantum CCR measurements in dynamics studies of proteins. We compile a list of all experiments proposed for CCR rate measurements, provide an overview of the theory with a focus on protein dynamics, and present applications to various protein systems.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17 Avenue, Aurora, CO 80045, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Laurimer Street Denver, CO 80204, United States
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Rout AK, Wu X, Starich MR, Strub MP, Hammer JA, Tjandra N. The Structure of Melanoregulin Reveals a Role for Cholesterol Recognition in the Protein's Ability to Promote Dynein Function. Structure 2018; 26:1373-1383.e4. [PMID: 30174147 DOI: 10.1016/j.str.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 06/12/2018] [Accepted: 07/24/2018] [Indexed: 01/24/2023]
Abstract
Melanoregulin (Mreg) is a small, highly charged, multiply palmitoylated protein present on the membrane of melanosomes. Mreg is implicated in the transfer of melanosomes from melanocytes to keratinocytes, and in promoting the microtubule minus end-directed transport of these organelles. The possible molecular function of Mreg was identified by solving its structure using nuclear magnetic resonance (NMR) spectroscopy. Mreg contains six α helices forming a fishhook-like fold in which positive and negative charges occupy opposite sides of the protein's surface and sandwich a putative, cholesterol recognition sequence (CRAC motif). Mreg containing a point mutation within its CRAC motif still targets to late endosomes/lysosomes, but no longer promotes their microtubule minus end-directed transport. Moreover, wild-type Mreg does not promote the microtubule minus end-directed transport of late endosomes/lysosomes in cells transiently depleted of cholesterol. Finally, reversing the charge of three clustered acidic residues partially inhibits Mreg's ability to drive these organelles to microtubule minus ends.
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Affiliation(s)
- Ashok K Rout
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xufeng Wu
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary R Starich
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A Hammer
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Fenwick RB, Vögeli B. Detection of Correlated Protein Backbone and Side-Chain Angle Fluctuations. Chembiochem 2017; 18:2016-2021. [PMID: 28771902 DOI: 10.1002/cbic.201700312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 11/09/2022]
Abstract
NMR methods for the characterization of local protein motions have attained a high level of sophistication. Measurement of the synchronization between those motions, however, poses a serious challenge. Such correlated motions are one of the underlying mechanisms for the propagation of local changes to remote sites and as such for information transfer. Here, we demonstrate the experimental detection of the synchronization of motion over an intermediate range. To that purpose, we designed pulse sequences for the measurement of cross-correlated relaxation between the backbone HN -N and side-chain Hβ -Cβ dipoles in Ile, Thr, and Val in the protein GB3. These bonds are related through two and three intervening dihedral angles. We show that the correlated motions inherent in a structural ensemble obtained from a large and diverse array of NMR probes are in excellent agreement with our measurements.
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Affiliation(s)
- R Bryn Fenwick
- The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, Research Center 1 South, Room 9103, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
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11
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Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH. Microsecond Dynamics in Ubiquitin Probed by Solid-State 15
N NMR Spectroscopy R
1ρ
Relaxation Experiments under Fast MAS (60-110 kHz). Chemistry 2017; 23:9425-9433. [DOI: 10.1002/chem.201701738] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Susanne Penzel
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Alons Lends
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
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Vögeli B. Cross-correlated relaxation rates between protein backbone H-X dipolar interactions. JOURNAL OF BIOMOLECULAR NMR 2017; 67:211-232. [PMID: 28286915 DOI: 10.1007/s10858-017-0098-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 02/19/2017] [Indexed: 06/06/2023]
Abstract
The relaxation interference between dipole-dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive HN-N and Hα-Cα dipole-dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5-3% of the entire value ranges.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Research Center 1 South, Room 9103, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
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Ravera E, Sgheri L, Parigi G, Luchinat C. A critical assessment of methods to recover information from averaged data. Phys Chem Chem Phys 2017; 18:5686-701. [PMID: 26565805 DOI: 10.1039/c5cp04077a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conformational heterogeneity is key to the function of many biomacromolecules, but only a few groups have tried to characterize it until recently. Now, thanks to the increased throughput of experimental data and the increased computational power, the problem of the characterization of protein structural variability has become more and more popular. Several groups have devoted their efforts in trying to create quantitative, reliable and accurate protocols for extracting such information from averaged data. We analyze here different approaches, discussing strengths and weaknesses of each. All approaches can roughly be clustered into two groups: those satisfying the maximum entropy principle and those recovering ensembles composed of a restricted number of molecular conformations. In the first case, the solution focuses on the features that are common to all the infinite solutions satisfying the experimental data; in the second case, the reconstructed ensemble shows the conformational regions where a large probability can be placed. The upper limits for conformational probabilities (MaxOcc) can also be calculated. We also give an overview of the mainstream experimental observables, with considerations on the assumptions underlying their usage.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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15
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Vögeli B, Olsson S, Güntert P, Riek R. The Exact NOE as an Alternative in Ensemble Structure Determination. Biophys J 2016; 110:113-26. [PMID: 26745415 DOI: 10.1016/j.bpj.2015.11.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022] Open
Abstract
The structure-function paradigm is increasingly replaced by the structure-dynamics-function paradigm. All protein activity is steered by the interplay between enthalpy and entropy. Conformational dynamics serves as a proxy of conformational entropy. Therefore, it is essential to study not only the average conformation but also the spatial sampling of a protein on all timescales. To this purpose, we have established a protocol for determining multiple-state ensembles of proteins based on exact nuclear Overhauser effects (eNOEs). We have recently extended our previously reported eNOE data set for the protein GB3 by a very large set of backbone and side-chain residual dipolar couplings and three-bond J couplings. Here, we demonstrate that at least four structural states are required to represent the complete data set by dissecting the contributions to the CYANA target function, which quantifies restraint violations in structure calculation. We present a four-state ensemble of GB3, which largely preserves the characteristics obtained from eNOEs only. Due to the abundance of the input data, the ensemble and χ(1) angles in particular are well suited for cross-validation of the input data and comparison to x-ray structures. Principal component analysis is used to automatically identify and validate relevant states of the ensembles. Overall, our findings suggest that eNOEs are a valuable alternative to traditional NMR probes in spatial elucidation of proteins.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
| | - Simon Olsson
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
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16
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Fenwick RB, Schwieters CD, Vögeli B. Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions. J Am Chem Soc 2016; 138:8412-21. [PMID: 27331619 PMCID: PMC5055379 DOI: 10.1021/jacs.6b01447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions, and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the micro- to millisecond time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive H(N)-N and H(α)-C(α) bonds, which act as a proxy for the peptide planes and the side chains, respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data, we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR, we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general, we find that the bond motions are on average slightly correlated and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated, and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices, there is also a weak correlation in the H(N)-N bonds. The degree of correlation involving H(α)-C(α) bonds is directly affected by side-chain fluctuations, whereas loops show complex and nonuniform behavior.
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Affiliation(s)
- R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Spain
- The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Building 12A Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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17
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Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
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Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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18
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Gu Y, Li DW, Brüschweiler R. NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment. J Chem Theory Comput 2015; 10:2599-607. [PMID: 26580780 DOI: 10.1021/ct500181v] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Functional protein motions covering a wide range of time scales can be studied, among other techniques, by NMR and by molecular dynamics (MD) computer simulations. MD simulations of proteins now routinely extend into the hundreds of nanoseconds time scale range exceeding the overall tumbling correlation times of proteins in solution by several orders of magnitude. This provides a unique opportunity to rigorously validate these simulations by quantitative comparison with model-free order parameters derived from NMR relaxation experiments. However, presently there is no consensus on how such a comparison is best done. We address here how this can be accomplished in a way that is both efficient and objective. For this purpose, we analyze (15)N R1 and R2 and heteronuclear {(1)H}-(15)N NOE NMR relaxation parameters computed from 500 ns MD trajectories of 10 different protein systems using the model-free analysis. The resulting model-free S(2) order parameters are then used as targets for S(2) values computed directly from the trajectories by the iRED method by either averaging over blocks of variable lengths or by using exponentially weighted snapshots (wiRED). We find that the iRED results are capable of reproducing the target S(2) values with high accuracy provided that the averaging window is chosen 5 times the length of the overall tumbling correlation time. These results provide useful guidelines for the derivation of NMR order parameters from MD for a meaningful comparison with their experimental counterparts.
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Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
| | - Da-Wei Li
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
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19
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Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3. Data Brief 2015; 5:99-106. [PMID: 26504890 PMCID: PMC4576366 DOI: 10.1016/j.dib.2015.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 01/26/2023] Open
Abstract
We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE) distance limits, residual dipolar couplings (RDCs) and scalar (J) couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.
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20
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Vögeli B, Olsson S, Riek R, Güntert P. Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics. J Struct Biol 2015. [DOI: 10.1016/j.jsb.2015.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Lamley JM, Lougher MJ, Sass HJ, Rogowski M, Grzesiek S, Lewandowski JR. Unraveling the complexity of protein backbone dynamics with combined (13)C and (15)N solid-state NMR relaxation measurements. Phys Chem Chem Phys 2015; 17:21997-2008. [PMID: 26234369 DOI: 10.1039/c5cp03484a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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22
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Olsson S, Ekonomiuk D, Sgrignani J, Cavalli A. Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings. J Am Chem Soc 2015; 137:6270-8. [PMID: 25895902 DOI: 10.1021/jacs.5b01289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are important probes in structural biology, but their analysis is often complicated by the determination of an alignment tensor or its associated assumptions. We here apply the maximum entropy principle to derive a tensor-free formalism which allows for direct, dynamic analysis of RDCs and holds the classic tensor formalism as a special case. Specifically, the framework enables us to robustly analyze data regardless of whether a clear separation of internal and overall dynamics is possible. Such a separation is often difficult in the core subjects of current structural biology, which include multidomain and intrinsically disordered proteins as well as nucleic acids. We demonstrate the method is tractable and self-consistent and generalizes to data sets comprised of observations from multiple different alignment conditions.
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Affiliation(s)
- Simon Olsson
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,‡Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Dariusz Ekonomiuk
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,§Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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23
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van den Bedem H, Fraser JS. Integrative, dynamic structural biology at atomic resolution--it's about time. Nat Methods 2015; 12:307-18. [PMID: 25825836 PMCID: PMC4457290 DOI: 10.1038/nmeth.3324] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/21/2015] [Indexed: 12/18/2022]
Abstract
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.
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Affiliation(s)
- Henry van den Bedem
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
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24
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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25
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Allison JR, Rivers RC, Christodoulou JC, Vendruscolo M, Dobson CM. A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein. Biochemistry 2014; 53:7170-83. [PMID: 25389903 PMCID: PMC4245978 DOI: 10.1021/bi5009326] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/25/2014] [Indexed: 12/02/2022]
Abstract
α-Synuclein is an intrinsically disordered protein whose aggregation is implicated in Parkinson's disease. A second member of the synuclein family, β-synuclein, shares significant sequence similarity with α-synuclein but is much more resistant to aggregation. β-Synuclein is missing an 11-residue stretch in the central non-β-amyloid component region that forms the core of α-synuclein amyloid fibrils, yet insertion of these residues into β-synuclein to produce the βSHC construct does not markedly increase the aggregation propensity. To investigate the structural basis of these different behaviors, quantitative nuclear magnetic resonance data, in the form of paramagnetic relaxation enhancement-derived interatomic distances, are combined with molecular dynamics simulations to generate ensembles of structures representative of the solution states of α-synuclein, β-synuclein, and βSHC. Comparison of these ensembles reveals that the differing aggregation propensities of α-synuclein and β-synuclein are associated with differences in the degree of residual structure in the C-terminus coupled to the shorter separation between the N- and C-termini in β-synuclein and βSHC, making protective intramolecular contacts more likely.
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Affiliation(s)
| | | | | | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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26
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Touw WG, Vriend G. BDB: Databank of PDB files with consistent B-factors. Protein Eng Des Sel 2014; 27:457-62. [DOI: 10.1093/protein/gzu044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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An L, Wang Y, Zhang N, Yan S, Bax A, Yao L. Protein apparent dielectric constant and its temperature dependence from remote chemical shift effects. J Am Chem Soc 2014; 136:12816-9. [PMID: 25192058 PMCID: PMC4183759 DOI: 10.1021/ja505852b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A NMR protocol is introduced that
permits accurate measurement
of minute, remote chemical shift perturbations (CSPs), caused by a
mutation-induced change in the electric field. Using protein GB3 as
a model system, 1HN CSPs in K19A and K19E mutants
can be fitted to small changes in the electric field at distal sites
in the protein using the Buckingham equation, yielding an apparent
dielectric constant εa of 8.6 ± 0.8 at 298 K.
These CSPs, and their derived εa value, scale strongly
with temperature. For example, CSPs at 313 K are about ∼30%
smaller than those at 278 K, corresponding to an effective εa value of about 7.3 at 278 K and 10.5 at 313 K. Molecular
dynamics simulations in explicit solvent indicate that solvent water
makes a significant contribution to εa.
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Affiliation(s)
- Liaoyuan An
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101, China
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28
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Olsson S, Vögeli BR, Cavalli A, Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K, Hamelryck T. Probabilistic Determination of Native State Ensembles of Proteins. J Chem Theory Comput 2014; 10:3484-91. [DOI: 10.1021/ct5001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Olsson
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Beat Rolf Vögeli
- Laboratory
of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Wouter Boomsma
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Ferkinghoff-Borg
- Cellular
Signal Integration Group, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Hamelryck
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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29
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30
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Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:958-67. [PMID: 24699641 PMCID: PMC4306559 DOI: 10.1107/s1399004713034160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/18/2013] [Indexed: 11/12/2022]
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
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Affiliation(s)
- Mauro Rinaldelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Vito Calderone
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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31
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Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:53-59. [PMID: 24656080 DOI: 10.1016/j.jmr.2013.11.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Celestine Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Martina Minges
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, 192-0397 Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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32
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Vögeli B. The nuclear Overhauser effect from a quantitative perspective. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 78:1-46. [PMID: 24534087 DOI: 10.1016/j.pnmrs.2013.11.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/13/2013] [Indexed: 05/26/2023]
Abstract
The nuclear Overhauser enhancement or effect (NOE) is the most important measure in liquid-state NMR with macromolecules. Thus, the NOE is the subject of numerous reviews and books. Here, the NOE is revisited in light of our recently introduced measurements of exact nuclear Overhauser enhancements (eNOEs), which enabled the determination of multiple-state 3D protein structures. This review encompasses all relevant facets from the theoretical considerations to the use of eNOEs in multiple-state structure calculation. Important aspects include a detailed presentation of the relaxation theory relevant for the nuclear Overhauser effect, the estimation of the correction for spin diffusion, the experimental determination of the eNOEs, the conversion of eNOE rates into distances and validation of their quality, the distance-restraint classification and the protocols for calculation of structures and ensembles.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, HCI F217, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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33
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Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, Gutmanas A. An overview of tools for the validation of protein NMR structures. JOURNAL OF BIOMOLECULAR NMR 2014; 58:259-285. [PMID: 23877928 DOI: 10.1007/s10858-013-9750-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).
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Affiliation(s)
- Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK,
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34
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Vammi V, Lin TL, Song G. Enhancing the quality of protein conformation ensembles with relative populations. JOURNAL OF BIOMOLECULAR NMR 2014; 58:209-225. [PMID: 24519023 DOI: 10.1007/s10858-014-9818-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 01/31/2014] [Indexed: 06/03/2023]
Abstract
The function and dynamics of many proteins are best understood not from a single structure but from an ensemble. A high quality ensemble is necessary for accurately delineating protein dynamics. However, conformations in an ensemble are generally given equal weights. Few attempts were made to assign relative populations to the conformations, mainly due to the lack of right experimental data. Here we propose a method for assigning relative populations to ensembles using experimental residue dipolar couplings (RDC) as constraints, and show that relative populations can significantly enhance an ensemble's ability in representing the native states and dynamics. The method works by identifying conformation states within an ensemble and assigning appropriate relative populations to them. Each of these conformation states is represented by a sub-ensemble consisting of a subset of the conformations. Application to the ubiquitin X-ray ensemble clearly identifies two key conformation states, with relative populations in excellent agreement with previous work. We then apply the method to a reprotonated ERNST ensemble that is enhanced with a switched conformation, and show that as a result of population reweighting, not only the reproduction of RDCs is significantly improved, but common conformational features (particularly the dihedral angle distributions of ϕ 53 and ψ 52) also emerge for both the X-ray ensemble and the reprotonated ERNST ensemble.
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Affiliation(s)
- Vijay Vammi
- Department of Computer Science, Bioinformatics and Computational Biology Program, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA,
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Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proc Natl Acad Sci U S A 2014; 111:E445-54. [PMID: 24474795 DOI: 10.1073/pnas.1323440111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond-nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S(2)) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements.
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Fragai M, Luchinat C, Parigi G, Ravera E. Conformational freedom of metalloproteins revealed by paramagnetism-assisted NMR. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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Chakravorty DK, Wang B, Lee CW, Guerra AJ, Giedroc DP, Merz KM. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. JOURNAL OF BIOMOLECULAR NMR 2013; 56:125-137. [PMID: 23609042 PMCID: PMC3773525 DOI: 10.1007/s10858-013-9729-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.
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Affiliation(s)
- Dhruva K. Chakravorty
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Bing Wang
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Chul Won Lee
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Alfredo J. Guerra
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Kenneth M. Merz
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
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de Magalhães MTQ, Barbosa EA, Prates MV, Verly RM, Munhoz VHO, de Araújo IE, Bloch C. Conformational and functional effects induced by D- and L-amino acid epimerization on a single gene encoded peptide from the skin secretion of Hypsiboas punctatus. PLoS One 2013; 8:e59255. [PMID: 23565145 PMCID: PMC3614549 DOI: 10.1371/journal.pone.0059255] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 02/12/2013] [Indexed: 11/19/2022] Open
Abstract
Skin secretion of Hypsiboas punctatus is the source of a complex mixture of bioactive compounds where peptides and small proteins prevail, similarly to many other amphibians. Among dozens of molecules isolated from H. punctatus in a proteomic based approach, we report here the structural and functional studies of a novel peptide named Phenylseptin (FFFDTLKNLAGKVIGALT-NH2) that was purified as two naturally occurring D- and L-Phes configurations. The amino acid epimerization and C-terminal amidation for both molecules were confirmed by a combination of techniques including reverse-phase UFLC, ion mobility mass spectrometry, high resolution MS/MS experiments, Edman degradation, cDNA sequencing and solid-phase peptide synthesis. RMSD analysis of the twenty lowest-energy (1)H NMR structures of each peptide revealed a major 90° difference between the two backbones at the first four N-terminal residues and substantial orientation changes of their respective side chains. These structural divergences were considered to be the primary cause of the in vitro quantitative differences in antimicrobial activities between the two molecules. Finally, both molecules elicited equally aversive reactions in mice when delivered orally, an effect that depended entirely on peripheral gustatory pathways.
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Affiliation(s)
- Mariana T. Q. de Magalhães
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília-Distrito Federal, Brasil
- Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brasil
- The John B. Pierce Laboratory, New Haven, Connecticut, United States of America
| | - Eder A. Barbosa
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília-Distrito Federal, Brasil
- Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brasil
| | - Maura V. Prates
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília-Distrito Federal, Brasil
| | - Rodrigo M. Verly
- Instituto de Química, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
- Departamento de Química Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
| | - Victor Hugo O. Munhoz
- Instituto de Química, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Ivan E. de Araújo
- The John B. Pierce Laboratory, New Haven, Connecticut, United States of America
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília-Distrito Federal, Brasil
- * E-mail: ,
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40
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Vögeli B, Güntert P, Riek R. Multiple-state ensemble structure determination from eNOE spectroscopy. Mol Phys 2013. [DOI: 10.1080/00268976.2012.728257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Vögeli B, Kazemi S, Güntert P, Riek R. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs. Nat Struct Mol Biol 2012; 19:1053-7. [DOI: 10.1038/nsmb.2355] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 07/06/2012] [Indexed: 11/09/2022]
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42
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Allison JR. Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data. Biophys Rev 2012; 4:189-203. [PMID: 28510078 DOI: 10.1007/s12551-012-0087-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022] Open
Abstract
The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties.
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Affiliation(s)
- Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural Sciences, Massey University Albany, Albany Highway, Auckland, 0632, New Zealand.
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Bertini I, Ferella L, Luchinat C, Parigi G, Petoukhov MV, Ravera E, Rosato A, Svergun DI. MaxOcc: a web portal for maximum occurrence analysis. JOURNAL OF BIOMOLECULAR NMR 2012; 53:271-280. [PMID: 22639196 DOI: 10.1007/s10858-012-9638-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at http://py-enmr.cerm.unifi.it/access/index/maxocc . It can be used freely upon registration to the grid with a digital certificate.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy.
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Reichert D, Zinkevich T, Saalwächter K, Krushelnitsky A. The relation of the X-ray B-factor to protein dynamics: insights from recent dynamic solid-state NMR data. J Biomol Struct Dyn 2012; 30:617-27. [PMID: 22746382 DOI: 10.1080/07391102.2012.689695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In addressing the potential use of B-factors derived from X-ray scattering data of proteins for the understanding the (functional) dynamics of proteins, we present a comparison of B-factors of five different proteins (SH3 domain, Crh, GB1, ubiquitin and thioredoxin) with data from recent solid-state nuclear magnetic resonance experiments reflecting true (rotational) dynamics on well-defined timescales. Apart from trivial correlations involving mobile loop regions and chain termini, we find no significant correlation of B-factors with the dynamic data on any of the investigated timescales, concluding that there is no unique and general correlation of B-factors with the internal reorientational dynamics of proteins.
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Affiliation(s)
- Detlef Reichert
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, Halle, 06120, Germany.
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Tossavainen H, Koskela O, Jiang P, Ylänne J, Campbell ID, Kilpeläinen I, Permi P. Model of a Six Immunoglobulin-Like Domain Fragment of Filamin A (16–21) Built Using Residual Dipolar Couplings. J Am Chem Soc 2012; 134:6660-72. [DOI: 10.1021/ja2114882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helena Tossavainen
- Program in
Structural Biology
and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari
1, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Outi Koskela
- Laboratory of Organic Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Pengju Jiang
- Biochemistry Department, University of Oxford, Oxford, OX1 3QU
United Kingdom
- School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164 China
| | - Jari Ylänne
- Department of Biological
and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35,
FI-40014 Jyväskylä, Finland
| | - Iain D. Campbell
- Biochemistry Department, University of Oxford, Oxford, OX1 3QU
United Kingdom
| | - Ilkka Kilpeläinen
- Laboratory of Organic Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Perttu Permi
- Program in
Structural Biology
and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari
1, P.O. Box 65, FI-00014 Helsinki, Finland
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46
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Shapiro YE, Meirovitch E. Slowly Relaxing Local Structure (SRLS) Analysis of 15N–H Relaxation from the Prototypical Small Proteins GB1 and GB3. J Phys Chem B 2012; 116:4056-68. [DOI: 10.1021/jp300245k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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47
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Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1339-55. [PMID: 22089251 PMCID: PMC3222826 DOI: 10.1007/s00249-011-0754-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 09/06/2011] [Accepted: 09/14/2011] [Indexed: 10/31/2022]
Abstract
We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future.
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48
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The catalytic domain of MMP-1 studied through tagged lanthanides. FEBS Lett 2011; 586:557-67. [DOI: 10.1016/j.febslet.2011.09.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/12/2011] [Accepted: 09/12/2011] [Indexed: 11/22/2022]
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49
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Miletti T, Farber PJ, Mittermaier A. Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation. JOURNAL OF BIOMOLECULAR NMR 2011; 51:71-82. [PMID: 21947916 DOI: 10.1007/s10858-011-9542-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
We have characterized the backbone dynamics of NADH oxidase from Thermus thermophilus (NOX) using a recently-developed suite of NMR experiments designed to isolate exchange broadening, together with (15)N R (1), R (1ρ ), and {(1)H}-(15)N steady-state NOE relaxation measurements performed at 11.7 and 18.8 T. NOX is a 54 kDa homodimeric enzyme that belongs to a family of structurally homologous flavin reductases and nitroreductases with many potential biotechnology applications. Prior studies have suggested that flexibility is involved in the catalytic mechanism of the enzyme. The active site residue W47 was previously identified as being particularly important, as its level of solvent exposure correlates with enzyme activity, and it was observed to undergo "gating" motions in computer simulations. The NMR data are consistent with these findings. Signals from W47 are dynamically broadened beyond detection and several other residues in the active site have significant R ( ex ) contributions to transverse relaxation rates. In addition, the backbone of S193, whose side chain hydroxyl proton hydrogen bonds directly with the FMN cofactor, exhibits extensive mobility on the ns-ps timescale. We hypothesize that these motions may facilitate structural rearrangements of the active site that allow NOX to accept both FMN and FAD as cofactors.
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Affiliation(s)
- Teresa Miletti
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
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50
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Vögeli B. How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cα-C'/H N-N cross-correlated relaxation. JOURNAL OF BIOMOLECULAR NMR 2011; 50:315-329. [PMID: 21638015 DOI: 10.1007/s10858-011-9519-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 05/17/2011] [Indexed: 05/30/2023]
Abstract
Highly precise and accurate measurements of very small NMR cross-correlated relaxation rates, namely those between protein H (i) (N) -N(i) and C (i-1) (α) -C(i-1)' dipoles, are demonstrated with an error of 0.03 s(-1) for GB3. Because the projection angles between the two dipole vectors are very close to the magic angle the rates range only from -0.2 to +0.2 s(-1). Small changes of the average vector orientations have a dramatic impact on the relative values. The rates suggest deviation from idealized peptide plane geometry caused by twists around the C'-N bonds and/or pyramidalization of the nitrogen atoms. A clear alternating pattern along the sequence is observed in β strands 1, 3 and 4 of GB3, where the side chains of almost all residues with large positive rates are solvent exposed. In the α helix all rates are relatively large and positive. Some of the currently most accurate structures of GB3 determined by both high resolution X-ray crystallography and NMR are in satisfactory agreement with the experimental rates in the helix and β strand 3, but not in the loops and the two central strands of the sheet for which no alternating pattern is predicted.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zürich, Switzerland.
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